Zoology or Animal Biology

Why do most proteins have an ideal pH between 4 and 8?


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Any protein will have evolved to have an optimum pH that matches the environment it is most commonly found in. This does mean that not all proteins have an ideal pH between 4 and 8. For example, almost all eukaryotic cells contain digestive enzymes that operate best at very low pH and not very well at pH 4-8, so that they won't digest their own cells, which will usually be at pH 7.

Whatever the ideal pH happens to be, the reason for it is always the same:

* Proteins fold into particular shapes that are vital for their function. * The shape a protein will fold into is determined by its amino acid sequence, since different amino acids have different properties. * Each amino acid has a 'side chain' sticking out of the main polypeptide chain, which will have specific chemical properties capable of forming certain interactions with other amino acids in the protein (as well as with water and other molecules).

* It is these intramolecular forces (interactions between different amino acids within a protein) that are responsible for producing and maintaining the shape of the protein. The forces are:

* Hydrogen bonds - weak bonds between slightly positively charged hydrogen and slightly negatively charged atoms (such as oxygen). * Electrostatic interactions - weak attractive forces between charged regions of the protein, including only small charges resulting from polar bonds. * Disulphide bridges * Hydrophobic interactions

* Hydrophobic interactions are not sufficient to hold a protein in a particular shape, only to pull the protein into a ball to help it fold into the correct shape. * Hydrogen bonds and electrostatic interactions are dependent on interactions between charges. pH is a measure of the concentration of hydrogen ions, which are positively charged. If there were more hydrogen ions in the solution than the protein was designed for, these ions would compete for the interactions holding the protein together, as well as protonating groups that need to be deprotonated to form important intramolecular interactions (eg nitrogen). Equally, if there were too few hydrogen ions in the solution, the same interactions would disrupted by the relatively high concentration of hydroxide (OH) ions, and important protonated groups may become deprotonated.

* Disruption of the interactions in either case will lead to some of the protein losing its ability to be held in a certain shape, which then reduces it's catalytic activity (as catalytic activity relies on the shape). The loss of activity will be proportional to the extent of the disruptions, which will in turn be proportional to the extent of the change in pH. * Disulphide bonds would also be reduced (broken) at very low pH. * Therefore, all proteins have a pH at which they have been designed to work that they will work very well at. The further away from this pH the solution gets, the more of the proteins will be effected by the change, until eventually they are all completely denatured. This concept is similar to the collision theory, in that a small change in pH will reduce activity, but not significantly, because very few of the increased hydrogen/hydroxide ions will actually be competing for the intramolecular interactions at any one time. In the specific case of pH being between 4 and 8, this is because most cells have an interior pH of between 4 and 8, so a lot of proteins need to operate best in this range (usually pH 7).